Summarise taxonmic distribution in the EMP dataset

true 23 July, 2021

Summarise the taxonmic distribution across different sample types in the Earth Microbiome Project

The Earth Microbiome Project (EMP) is collaborative effort to curate and characterise microbial taxonomy and function on Earth (Thompson et al. 2017).
The aim of this script is to summarise the taxonomic distribution across different sample types, as defined by the EMP. The script summarises phyla by default but can also summarise the sequences at different taxonomy levels. The script uses the 3rd classification level of the EMP Ontology (empo_3), but this can also be altered.

Set main parameters and download data tables from the EMP FTP site

ftp <- "ftp://ftp.microbio.me/emp/release1/"
biom_file <- "emp_cr_silva_16S_123.subset_10k.biom"
map_file <- "emp_qiime_mapping_subset_10k.tsv"
new_map_file <- "emp_qiime_mapping_subset_10k_noBLNK.csv"
Rank <- "Phylum"
Grouping_var <- "empo_3"
EMPO_levels2keep <- c("Soil (non-saline)", "Plant rhizosphere", "Animal corpus", "Water (saline)", "Sediment (saline)", "Water (non-saline)", "Hypersaline (saline)", "Sediment (non-saline)", "Animal distal gut", "Animal proximal gut", "Aerosol (non-saline)", "Animal secretion", "Animal surface", "Plant corpus", "Surface (non-saline)", "Plant surface", "Surface (saline)") # remove unwanted environments
s_size = 1000 # genomes to sample per community
biom_ftp <- paste0(ftp, "otu_tables/closed_ref_silva/", biom_file)
map_ftp <- paste0(ftp, "mapping_files/", map_file)
download.file(biom_ftp, biom_file)
download.file(map_ftp, map_file)

# fill-in missing values with NA, convert to CSV
system("awk 'BEGIN { FS = OFS = \"\t\" } { for(i=1; i<=NF; i++) if($i ~ /^ *$/) $i = \"NA\" }; 1' emp_qiime_mapping_subset_10k.tsv  |  awk 'BEGIN { FS=\",\"; OFS=\";\" } {$1=$1; print}' |  awk 'BEGIN { FS=\"\t\"; OFS=\",\" } {$1=$1; print}' > emp_qiime_mapping_subset_10k_noBLNK.csv")

Generate a phyloseq object from the biom and (modified) map files

(EMP_otu_tax <- import_biom(biom_file, parseFunction = parse_taxonomy_silva_128, 
                            parallel = TRUE))
## phyloseq-class experiment-level object
## otu_table()   OTU Table:          [ 126730 taxa and 10000 samples ]:
## tax_table()   Taxonomy Table:     [ 126730 taxa by 7 taxonomic ranks ]:
## taxa are rows
read_csv(new_map_file,
                    trim_ws = TRUE) %>% 
  column_to_rownames("#SampleID") %>% 
  sample_data() ->
  EMP_map

EMP <- merge_phyloseq(EMP_otu_tax, EMP_map)

# for debugging and testing
# EMP %>%
#   subset_samples(empo_3 %in% EMPO_levels2keep) %>%
#   prune_samples(sample_names(.)[sample(1:nsamples(.), 100)], .) %>%
#   phyloseq::filter_taxa(., function(x) sum(x) > 0, TRUE) %>%
#   prune_taxa(taxa_names(.)[sample(1:ntaxa(.), 1000)], .) ->
#   EMP_subset

EMP %>% 
  PS_merge_samples(grouping_name = Grouping_var, fun = "mean") ->
  EMP_merge

save(EMP, file = paste0("EMP.RDS"))
save(EMP_merge, file = paste0("EMP_merge.RDS"))
# load("./EMP.RDS")
# load("./EMP_merge.RDS")

Generate a summary table of taxonomic distributions across sample types

# summarise abundance by environment and phylum
EMP %>%
  tax_glom(taxrank = Rank) %>%                     # agglomerate at 'Rank' level
  psmelt() %>%                                         # Melt to long format
  arrange(Rank) %>%                                  # arrange by 'Rank'
  group_by_at(c(Grouping_var, Rank)) %>% 
  # summarise and create a column with the relative abundance
  summarise(`Abundance (mean)` = mean(Abundance),
            n = n(),  # calculates the sample size per group
            SD = sd(Abundance, na.rm = T)) %>%  # calculates the standard error of each group
  mutate(Freq = (100 * `Abundance (mean)` / sum(`Abundance (mean)`)),
         `Freq SD` = (100 * SD / sum(`Abundance (mean)`))) -> # abundance per empo_3 cat
  taxa_sum_df

# determine the phylum order by decreasing abundance (for plotting)
EMP_merge %>%
  tax_glom(taxrank = Rank) %>%                     # agglomerate at 'Rank' level
    transform_sample_counts(., function(x) x / sum(x) * 100) %>% 
  psmelt() %>%                                        # Melt to long format
  arrange(Rank)  %>%                                  # arrange by 'Rank'
  group_by_at(c("OTU", Rank)) %>% 
  summarise(`Abundance (mean)` = mean(Abundance)) %>%
  arrange(`Abundance (mean)`) ->
  Rank_order

# print summary table
taxa_sum_df %>% 
  filter(`Abundance (mean)` != 0) %>%
  kable(., digits = c( 0, 1)) %>%
  kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = F)
empo\_3 Phylum Abundance (mean) n SD Freq Freq SD
Aerosol (non-saline) Acidobacteria 811 81 1437 0.8 1
Aerosol (non-saline) Actinobacteria 8865 81 7179 8.7 7
Aerosol (non-saline) Aerophobetes 0 81 0 0.0 0
Aerosol (non-saline) Aminicenantes 1 81 9 0.0 0
Aerosol (non-saline) aquifer1 26 81 142 0.0 0
Aerosol (non-saline) Armatimonadetes 87 81 171 0.1 0
Aerosol (non-saline) Atribacteria 2 81 15 0.0 0
Aerosol (non-saline) Bacteroidetes 10186 81 9304 10.0 9
Aerosol (non-saline) Caldiserica 0 81 0 0.0 0
Aerosol (non-saline) Candidate division OP3 2 81 6 0.0 0
Aerosol (non-saline) Candidate division SR1 41 81 110 0.0 0
Aerosol (non-saline) Chlamydiae 7 81 38 0.0 0
Aerosol (non-saline) Chlorobi 8 81 36 0.0 0
Aerosol (non-saline) Chloroflexi 278 81 344 0.3 0
Aerosol (non-saline) Cloacimonetes 4 81 19 0.0 0
Aerosol (non-saline) Cyanobacteria 17601 81 46093 17.3 45
Aerosol (non-saline) Deferribacteres 0 81 1 0.0 0
Aerosol (non-saline) Deinococcus-Thermus 37 81 80 0.0 0
Aerosol (non-saline) Elusimicrobia 9 81 42 0.0 0
Aerosol (non-saline) Euryarchaeota 80 81 139 0.1 0
Aerosol (non-saline) Fibrobacteres 33 81 114 0.0 0
Aerosol (non-saline) Firmicutes 29439 81 27758 29.0 27
Aerosol (non-saline) Fusobacteria 877 81 1248 0.9 1
Aerosol (non-saline) GAL08 0 81 0 0.0 0
Aerosol (non-saline) Gemmatimonadetes 215 81 318 0.2 0
Aerosol (non-saline) Gracilibacteria 0 81 1 0.0 0
Aerosol (non-saline) Hyd24-12 0 81 0 0.0 0
Aerosol (non-saline) Hydrogenedentes 2 81 11 0.0 0
Aerosol (non-saline) JL-ETNP-Z39 0 81 3 0.0 0
Aerosol (non-saline) Latescibacteria 2 81 9 0.0 0
Aerosol (non-saline) Lentisphaerae 37 81 138 0.0 0
Aerosol (non-saline) Marinimicrobia (SAR406 clade) 6 81 37 0.0 0
Aerosol (non-saline) Microgenomates 0 81 0 0.0 0
Aerosol (non-saline) Miscellaneous Crenarchaeotic Group 0 81 1 0.0 0
Aerosol (non-saline) Nitrospirae 30 81 71 0.0 0
Aerosol (non-saline) Omnitrophica 0 81 0 0.0 0
Aerosol (non-saline) Parcubacteria 8 81 50 0.0 0
Aerosol (non-saline) PAUC34f 0 81 0 0.0 0
Aerosol (non-saline) Planctomycetes 221 81 325 0.2 0
Aerosol (non-saline) Proteobacteria 31337 81 32672 30.8 32
Aerosol (non-saline) Saccharibacteria 28 81 48 0.0 0
Aerosol (non-saline) SHA-109 4 81 18 0.0 0
Aerosol (non-saline) SM2F11 0 81 0 0.0 0
Aerosol (non-saline) Spirochaetae 184 81 435 0.2 0
Aerosol (non-saline) Synergistetes 23 81 97 0.0 0
Aerosol (non-saline) TA06 0 81 0 0.0 0
Aerosol (non-saline) Tenericutes 179 81 269 0.2 0
Aerosol (non-saline) Thaumarchaeota 76 81 192 0.1 0
Aerosol (non-saline) Thermotogae 73 81 272 0.1 0
Aerosol (non-saline) TM6 12 81 78 0.0 0
Aerosol (non-saline) uncultured archaeon 0 162 0 0.0 0
Aerosol (non-saline) Verrucomicrobia 730 81 1062 0.7 1
Aerosol (non-saline) WCHB1-60 0 81 1 0.0 0
Aerosol (non-saline) WD272 20 81 86 0.0 0
Aerosol (non-saline) Woesearchaeota (DHVEG-6) 0 81 0 0.0 0
Animal corpus Acetothermia 0 322 1 0.0 0
Animal corpus Acidobacteria 122 322 1136 0.4 4
Animal corpus Actinobacteria 3285 322 9205 11.3 32
Animal corpus Aerophobetes 1 322 5 0.0 0
Animal corpus Aminicenantes 1 322 4 0.0 0
Animal corpus aquifer1 1 322 5 0.0 0
Animal corpus Aquificae 0 322 1 0.0 0
Animal corpus Armatimonadetes 8 322 102 0.0 0
Animal corpus Atribacteria 3 322 14 0.0 0
Animal corpus Bacteroidetes 928 322 6033 3.2 21
Animal corpus Caldiserica 0 322 0 0.0 0
Animal corpus Candidate division OP3 0 322 5 0.0 0
Animal corpus Candidate division SR1 0 322 2 0.0 0
Animal corpus Chlamydiae 0 322 4 0.0 0
Animal corpus Chlorobi 3 322 45 0.0 0
Animal corpus Chloroflexi 10 322 71 0.0 0
Animal corpus Cyanobacteria 962 322 3178 3.3 11
Animal corpus Deferribacteres 0 322 2 0.0 0
Animal corpus Deinococcus-Thermus 3 322 11 0.0 0
Animal corpus Elusimicrobia 0 322 1 0.0 0
Animal corpus Euryarchaeota 1 322 7 0.0 0
Animal corpus Fibrobacteres 0 322 2 0.0 0
Animal corpus Firmicutes 4863 322 6151 16.7 21
Animal corpus Fusobacteria 46 322 277 0.2 1
Animal corpus Gemmatimonadetes 9 322 84 0.0 0
Animal corpus GOUTA4 0 322 1 0.0 0
Animal corpus Gracilibacteria 0 322 0 0.0 0
Animal corpus Hyd24-12 0 322 2 0.0 0
Animal corpus Hydrogenedentes 0 322 2 0.0 0
Animal corpus JL-ETNP-Z39 0 322 1 0.0 0
Animal corpus Latescibacteria 0 322 0 0.0 0
Animal corpus LCP-89 0 322 0 0.0 0
Animal corpus Lentisphaerae 0 322 1 0.0 0
Animal corpus Marinimicrobia (SAR406 clade) 3 322 50 0.0 0
Animal corpus Microgenomates 0 322 0 0.0 0
Animal corpus Miscellaneous Crenarchaeotic Group 0 322 0 0.0 0
Animal corpus Nitrospirae 1 322 10 0.0 0
Animal corpus Parcubacteria 0 322 1 0.0 0
Animal corpus Planctomycetes 8 322 48 0.0 0
Animal corpus Proteobacteria 18728 322 15935 64.5 55
Animal corpus Saccharibacteria 1 322 10 0.0 0
Animal corpus SHA-109 0 322 0 0.0 0
Animal corpus SM2F11 0 322 1 0.0 0
Animal corpus Spirochaetae 2 322 22 0.0 0
Animal corpus Synergistetes 1 322 9 0.0 0
Animal corpus TA06 0 322 0 0.0 0
Animal corpus Tenericutes 25 322 79 0.1 0
Animal corpus Thaumarchaeota 2 322 12 0.0 0
Animal corpus Thermotogae 0 322 2 0.0 0
Animal corpus TM6 0 322 4 0.0 0
Animal corpus Verrucomicrobia 39 322 291 0.1 1
Animal corpus WCHB1-60 0 322 1 0.0 0
Animal corpus WD272 0 322 4 0.0 0
Animal corpus Woesearchaeota (DHVEG-6) 0 322 0 0.0 0
Animal distal gut Acidobacteria 36 953 405 0.1 1
Animal distal gut Actinobacteria 2515 953 9155 3.8 14
Animal distal gut Aerophobetes 0 953 0 0.0 0
Animal distal gut Aminicenantes 0 953 0 0.0 0
Animal distal gut aquifer1 0 953 5 0.0 0
Animal distal gut Armatimonadetes 4 953 34 0.0 0
Animal distal gut Atribacteria 0 953 0 0.0 0
Animal distal gut Bacteroidetes 13581 953 19188 20.6 29
Animal distal gut Caldiserica 0 953 1 0.0 0
Animal distal gut Candidate division OP3 0 953 1 0.0 0
Animal distal gut Candidate division SR1 2 953 48 0.0 0
Animal distal gut Chlamydiae 5 953 89 0.0 0
Animal distal gut Chlorobi 1 953 9 0.0 0
Animal distal gut Chloroflexi 27 953 113 0.0 0
Animal distal gut CKC4 50 953 604 0.1 1
Animal distal gut Cloacimonetes 0 953 0 0.0 0
Animal distal gut Cyanobacteria 1015 953 6320 1.5 10
Animal distal gut Deferribacteres 1 953 7 0.0 0
Animal distal gut Deinococcus-Thermus 9 953 102 0.0 0
Animal distal gut Elusimicrobia 11 953 54 0.0 0
Animal distal gut Euryarchaeota 218 953 611 0.3 1
Animal distal gut Fibrobacteres 8 953 138 0.0 0
Animal distal gut Firmicutes 27539 953 31837 41.8 48
Animal distal gut Fusobacteria 1273 953 5624 1.9 9
Animal distal gut Gemmatimonadetes 5 953 42 0.0 0
Animal distal gut GOUTA4 0 953 0 0.0 0
Animal distal gut Gracilibacteria 0 953 8 0.0 0
Animal distal gut Hydrogenedentes 0 953 1 0.0 0
Animal distal gut JL-ETNP-Z39 0 953 2 0.0 0
Animal distal gut Kazan-3B-09 0 953 0 0.0 0
Animal distal gut Latescibacteria 0 953 8 0.0 0
Animal distal gut LCP-89 0 953 0 0.0 0
Animal distal gut Lentisphaerae 122 953 368 0.2 1
Animal distal gut Marinimicrobia (SAR406 clade) 1 953 7 0.0 0
Animal distal gut Microgenomates 0 953 1 0.0 0
Animal distal gut Miscellaneous Crenarchaeotic Group 0 953 0 0.0 0
Animal distal gut Nitrospirae 3 953 56 0.0 0
Animal distal gut Omnitrophica 0 953 0 0.0 0
Animal distal gut Parcubacteria 0 953 0 0.0 0
Animal distal gut Parvarchaeota 0 953 0 0.0 0
Animal distal gut PAUC34f 0 953 0 0.0 0
Animal distal gut Planctomycetes 103 953 546 0.2 1
Animal distal gut Proteobacteria 17547 953 39480 26.7 60
Animal distal gut RsaHF231 1 953 16 0.0 0
Animal distal gut Saccharibacteria 3 953 10 0.0 0
Animal distal gut SHA-109 1 953 12 0.0 0
Animal distal gut SM2F11 0 953 0 0.0 0
Animal distal gut Spirochaetae 323 953 994 0.5 2
Animal distal gut Synergistetes 8 953 83 0.0 0
Animal distal gut TA06 0 953 2 0.0 0
Animal distal gut Tenericutes 718 953 2305 1.1 4
Animal distal gut Thaumarchaeota 11 953 161 0.0 0
Animal distal gut Thermotogae 0 953 0 0.0 0
Animal distal gut TM6 0 953 4 0.0 0
Animal distal gut uncultured archaeon 0 1906 0 0.0 0
Animal distal gut Verrucomicrobia 694 953 2031 1.1 3
Animal distal gut WCHB1-60 0 953 3 0.0 0
Animal distal gut WD272 0 953 4 0.0 0
Animal distal gut Woesearchaeota (DHVEG-6) 0 953 0 0.0 0
Animal proximal gut Acidobacteria 8 354 57 0.0 0
Animal proximal gut Actinobacteria 2280 354 7379 3.3 11
Animal proximal gut aquifer1 0 354 2 0.0 0
Animal proximal gut Aquificae 0 354 0 0.0 0
Animal proximal gut Armatimonadetes 0 354 2 0.0 0
Animal proximal gut Bacteroidetes 19428 354 23899 28.5 35
Animal proximal gut Caldiserica 0 354 0 0.0 0
Animal proximal gut Candidate division OP3 0 354 0 0.0 0
Animal proximal gut Candidate division SR1 1 354 14 0.0 0
Animal proximal gut Chlamydiae 0 354 3 0.0 0
Animal proximal gut Chlorobi 0 354 2 0.0 0
Animal proximal gut Chloroflexi 7 354 37 0.0 0
Animal proximal gut Cyanobacteria 951 354 2916 1.4 4
Animal proximal gut Deferribacteres 2 354 17 0.0 0
Animal proximal gut Deinococcus-Thermus 3 354 18 0.0 0
Animal proximal gut Elusimicrobia 0 354 2 0.0 0
Animal proximal gut Euryarchaeota 266 354 552 0.4 1
Animal proximal gut Fibrobacteres 135 354 429 0.2 1
Animal proximal gut Firmicutes 32369 354 30522 47.5 45
Animal proximal gut Fusobacteria 271 354 1866 0.4 3
Animal proximal gut Gemmatimonadetes 2 354 18 0.0 0
Animal proximal gut Gracilibacteria 1 354 11 0.0 0
Animal proximal gut Hydrogenedentes 0 354 0 0.0 0
Animal proximal gut Latescibacteria 0 354 1 0.0 0
Animal proximal gut Lentisphaerae 187 354 559 0.3 1
Animal proximal gut Marinimicrobia (SAR406 clade) 0 354 0 0.0 0
Animal proximal gut Nitrospirae 0 354 3 0.0 0
Animal proximal gut Omnitrophica 0 354 0 0.0 0
Animal proximal gut Parcubacteria 0 354 0 0.0 0
Animal proximal gut PAUC34f 0 354 0 0.0 0
Animal proximal gut Planctomycetes 367 354 1367 0.5 2
Animal proximal gut Proteobacteria 7614 354 12998 11.2 19
Animal proximal gut Saccharibacteria 1 354 4 0.0 0
Animal proximal gut SHA-109 3 354 28 0.0 0
Animal proximal gut SM2F11 0 354 0 0.0 0
Animal proximal gut Spirochaetae 1673 354 3375 2.5 5
Animal proximal gut Synergistetes 41 354 106 0.1 0
Animal proximal gut TA06 0 354 0 0.0 0
Animal proximal gut Tenericutes 275 354 668 0.4 1
Animal proximal gut Thaumarchaeota 3 354 16 0.0 0
Animal proximal gut Thermotogae 0 354 0 0.0 0
Animal proximal gut TM6 0 354 2 0.0 0
Animal proximal gut Verrucomicrobia 2322 354 5153 3.4 8
Animal proximal gut WCHB1-60 0 354 0 0.0 0
Animal proximal gut WD272 0 354 4 0.0 0
Animal proximal gut Woesearchaeota (DHVEG-6) 0 354 2 0.0 0
Animal secretion Acetothermia 0 917 0 0.0 0
Animal secretion Acidobacteria 124 917 522 0.3 1
Animal secretion Actinobacteria 5146 917 7378 10.5 15
Animal secretion Aerophobetes 0 917 2 0.0 0
Animal secretion Aminicenantes 0 917 1 0.0 0
Animal secretion aquifer1 46 917 134 0.1 0
Animal secretion Armatimonadetes 6 917 25 0.0 0
Animal secretion Atribacteria 0 917 2 0.0 0
Animal secretion Bacteroidetes 5469 917 7229 11.2 15
Animal secretion Caldiserica 0 917 0 0.0 0
Animal secretion Candidate division OP3 0 917 1 0.0 0
Animal secretion Candidate division SR1 39 917 243 0.1 0
Animal secretion Chlamydiae 2 917 24 0.0 0
Animal secretion Chlorobi 6 917 36 0.0 0
Animal secretion Chloroflexi 30 917 132 0.1 0
Animal secretion CKC4 0 917 0 0.0 0
Animal secretion Cloacimonetes 0 917 0 0.0 0
Animal secretion Crenarchaeota 0 917 0 0.0 0
Animal secretion Cyanobacteria 640 917 2632 1.3 5
Animal secretion Deferribacteres 0 917 2 0.0 0
Animal secretion Deinococcus-Thermus 19 917 131 0.0 0
Animal secretion Dictyoglomi 0 917 0 0.0 0
Animal secretion Elusimicrobia 1 917 4 0.0 0
Animal secretion Euryarchaeota 4 917 22 0.0 0
Animal secretion Fibrobacteres 1 917 4 0.0 0
Animal secretion Firmicutes 15784 917 16637 32.3 34
Animal secretion Fusobacteria 1970 917 3010 4.0 6
Animal secretion GAL08 0 917 0 0.0 0
Animal secretion Gemmatimonadetes 50 917 225 0.1 0
Animal secretion GOUTA4 0 917 0 0.0 0
Animal secretion Gracilibacteria 6 917 35 0.0 0
Animal secretion Hyd24-12 0 917 0 0.0 0
Animal secretion Hydrogenedentes 1 917 5 0.0 0
Animal secretion JL-ETNP-Z39 0 917 1 0.0 0
Animal secretion Kazan-3B-09 0 917 0 0.0 0
Animal secretion Latescibacteria 1 917 3 0.0 0
Animal secretion LCP-89 0 917 0 0.0 0
Animal secretion Lentisphaerae 2 917 7 0.0 0
Animal secretion Marinimicrobia (SAR406 clade) 1 917 11 0.0 0
Animal secretion Microgenomates 0 917 1 0.0 0
Animal secretion Miscellaneous Crenarchaeotic Group 0 917 0 0.0 0
Animal secretion Nitrospirae 8 917 33 0.0 0
Animal secretion OC31 0 917 0 0.0 0
Animal secretion Omnitrophica 0 917 0 0.0 0
Animal secretion Parcubacteria 0 917 5 0.0 0
Animal secretion PAUC34f 0 917 0 0.0 0
Animal secretion Planctomycetes 32 917 113 0.1 0
Animal secretion Proteobacteria 16921 917 21567 34.6 44
Animal secretion RsaHF231 0 917 1 0.0 0
Animal secretion Saccharibacteria 27 917 53 0.1 0
Animal secretion SHA-109 1 917 4 0.0 0
Animal secretion SM1K20 0 917 0 0.0 0
Animal secretion SM2F11 0 917 1 0.0 0
Animal secretion Spirochaetae 66 917 453 0.1 1
Animal secretion Synergistetes 5 917 21 0.0 0
Animal secretion TA06 0 917 0 0.0 0
Animal secretion Tenericutes 2426 917 5875 5.0 12
Animal secretion Thaumarchaeota 11 917 51 0.0 0
Animal secretion Thermotogae 0 917 1 0.0 0
Animal secretion TM6 1 917 4 0.0 0
Animal secretion Verrucomicrobia 58 917 220 0.1 0
Animal secretion WCHB1-60 0 917 3 0.0 0
Animal secretion WD272 0 917 3 0.0 0
Animal secretion Woesearchaeota (DHVEG-6) 0 917 0 0.0 0
Animal surface Acetothermia 0 987 0 0.0 0
Animal surface Acidobacteria 136 987 324 0.2 0
Animal surface Actinobacteria 9877 987 15253 14.0 22
Animal surface Aenigmarchaeota 0 987 0 0.0 0
Animal surface Aerophobetes 0 987 2 0.0 0
Animal surface Aminicenantes 0 987 8 0.0 0
Animal surface Ancient Archaeal Group(AAG) 0 987 0 0.0 0
Animal surface aquifer1 6 987 29 0.0 0
Animal surface Aquificae 0 987 8 0.0 0
Animal surface Armatimonadetes 27 987 86 0.0 0
Animal surface Atribacteria 0 987 4 0.0 0
Animal surface Bacteroidetes 5947 987 10204 8.5 15
Animal surface Caldiserica 0 987 0 0.0 0
Animal surface Candidate division OP3 0 987 2 0.0 0
Animal surface Candidate division SR1 6 987 33 0.0 0
Animal surface Chlamydiae 1 987 8 0.0 0
Animal surface Chlorobi 5 987 20 0.0 0
Animal surface Chloroflexi 71 987 216 0.1 0
Animal surface CKC4 1 987 15 0.0 0
Animal surface Cloacimonetes 0 987 3 0.0 0
Animal surface Crenarchaeota 0 987 0 0.0 0
Animal surface Cyanobacteria 1479 987 5813 2.1 8
Animal surface Deferribacteres 1 987 17 0.0 0
Animal surface Deinococcus-Thermus 109 987 566 0.2 1
Animal surface Elusimicrobia 1 987 15 0.0 0
Animal surface Euryarchaeota 11 987 46 0.0 0
Animal surface Fibrobacteres 3 987 41 0.0 0
Animal surface Firmicutes 15695 987 21419 22.3 30
Animal surface Fusobacteria 527 987 1585 0.7 2
Animal surface GAL08 0 987 0 0.0 0
Animal surface Gemmatimonadetes 66 987 194 0.1 0
Animal surface GOUTA4 0 987 0 0.0 0
Animal surface Gracilibacteria 4 987 44 0.0 0
Animal surface Hyd24-12 0 987 1 0.0 0
Animal surface Hydrogenedentes 3 987 17 0.0 0
Animal surface JL-ETNP-Z39 0 987 4 0.0 0
Animal surface Kazan-3B-09 0 987 0 0.0 0
Animal surface Latescibacteria 1 987 11 0.0 0
Animal surface LCP-89 0 987 0 0.0 0
Animal surface Lentisphaerae 4 987 15 0.0 0
Animal surface Marine Hydrothermal Vent Group(MHVG) 0 987 0 0.0 0
Animal surface Marinimicrobia (SAR406 clade) 0 987 4 0.0 0
Animal surface Microgenomates 0 987 5 0.0 0
Animal surface Miscellaneous Crenarchaeotic Group 0 987 1 0.0 0
Animal surface Nitrospirae 7 987 27 0.0 0
Animal surface OC31 0 987 0 0.0 0
Animal surface Omnitrophica 1 987 5 0.0 0
Animal surface Parcubacteria 1 987 4 0.0 0
Animal surface PAUC34f 0 987 5 0.0 0
Animal surface Planctomycetes 66 987 167 0.1 0
Animal surface Proteobacteria 34831 987 42565 49.5 61
Animal surface RsaHF231 0 987 3 0.0 0
Animal surface Saccharibacteria 4 987 19 0.0 0
Animal surface SHA-109 2 987 16 0.0 0
Animal surface SM1K20 0 987 0 0.0 0
Animal surface SM2F11 0 987 2 0.0 0
Animal surface Spirochaetae 13 987 42 0.0 0
Animal surface Synergistetes 2 987 12 0.0 0
Animal surface TA06 0 987 5 0.0 0
Animal surface Tenericutes 1176 987 4374 1.7 6
Animal surface Thaumarchaeota 10 987 34 0.0 0
Animal surface Thermodesulfobacteria 0 987 0 0.0 0
Animal surface Thermotogae 0 987 0 0.0 0
Animal surface TM6 2 987 12 0.0 0
Animal surface uncultured archaeon 0 1974 0 0.0 0
Animal surface Verrucomicrobia 203 987 573 0.3 1
Animal surface WCHB1-60 0 987 3 0.0 0
Animal surface WD272 1 987 10 0.0 0
Animal surface Woesearchaeota (DHVEG-6) 0 987 6 0.0 0
Hypersaline (saline) Acetothermia 239 13 410 0.3 1
Hypersaline (saline) Acidobacteria 1489 13 3558 2.1 5
Hypersaline (saline) Actinobacteria 3660 13 4586 5.1 6
Hypersaline (saline) Aenigmarchaeota 16 13 29 0.0 0
Hypersaline (saline) Aerophobetes 6 13 14 0.0 0
Hypersaline (saline) Aminicenantes 98 13 319 0.1 0
Hypersaline (saline) Armatimonadetes 83 13 178 0.1 0
Hypersaline (saline) Atribacteria 6 13 18 0.0 0
Hypersaline (saline) Bacteroidetes 8816 13 5918 12.4 8
Hypersaline (saline) Caldiserica 0 13 0 0.0 0
Hypersaline (saline) Candidate division OP3 28 13 46 0.0 0
Hypersaline (saline) Candidate division SR1 3 13 4 0.0 0
Hypersaline (saline) Chlamydiae 1 13 2 0.0 0
Hypersaline (saline) Chlorobi 36 13 68 0.0 0
Hypersaline (saline) Chloroflexi 1450 13 2570 2.0 4
Hypersaline (saline) Cloacimonetes 2 13 7 0.0 0
Hypersaline (saline) Crenarchaeota 0 13 0 0.0 0
Hypersaline (saline) Cyanobacteria 627 13 1253 0.9 2
Hypersaline (saline) Deferribacteres 30 13 46 0.0 0
Hypersaline (saline) Deinococcus-Thermus 338 13 413 0.5 1
Hypersaline (saline) Elusimicrobia 8 13 28 0.0 0
Hypersaline (saline) Euryarchaeota 23421 13 23500 32.9 33
Hypersaline (saline) Fibrobacteres 25 13 62 0.0 0
Hypersaline (saline) Firmicutes 510 13 786 0.7 1
Hypersaline (saline) Fusobacteria 6 13 9 0.0 0
Hypersaline (saline) GAL08 0 13 0 0.0 0
Hypersaline (saline) Gemmatimonadetes 374 13 725 0.5 1
Hypersaline (saline) Gracilibacteria 9 13 19 0.0 0
Hypersaline (saline) Hyd24-12 39 13 100 0.1 0
Hypersaline (saline) Hydrogenedentes 13 13 23 0.0 0
Hypersaline (saline) JL-ETNP-Z39 2 13 6 0.0 0
Hypersaline (saline) Kazan-3B-09 0 13 1 0.0 0
Hypersaline (saline) Latescibacteria 104 13 192 0.1 0
Hypersaline (saline) LCP-89 6 13 12 0.0 0
Hypersaline (saline) LD1-PA38 0 13 2 0.0 0
Hypersaline (saline) Lentisphaerae 243 13 404 0.3 1
Hypersaline (saline) Marinimicrobia (SAR406 clade) 124 13 244 0.2 0
Hypersaline (saline) Microgenomates 2 13 4 0.0 0
Hypersaline (saline) Miscellaneous Crenarchaeotic Group 21 13 41 0.0 0
Hypersaline (saline) Nanohaloarchaeota 135 13 233 0.2 0
Hypersaline (saline) Nitrospirae 127 13 316 0.2 0
Hypersaline (saline) Omnitrophica 24 13 35 0.0 0
Hypersaline (saline) Parcubacteria 31 13 39 0.0 0
Hypersaline (saline) PAUC34f 11 13 25 0.0 0
Hypersaline (saline) Planctomycetes 975 13 1604 1.4 2
Hypersaline (saline) Proteobacteria 25655 13 27096 36.1 38
Hypersaline (saline) Saccharibacteria 0 13 0 0.0 0
Hypersaline (saline) SHA-109 1 13 2 0.0 0
Hypersaline (saline) Spirochaetae 455 13 739 0.6 1
Hypersaline (saline) TA06 81 13 189 0.1 0
Hypersaline (saline) Tenericutes 1038 13 1989 1.5 3
Hypersaline (saline) Thaumarchaeota 435 13 628 0.6 1
Hypersaline (saline) Thermotogae 1 13 2 0.0 0
Hypersaline (saline) TM6 5 13 9 0.0 0
Hypersaline (saline) Verrucomicrobia 208 13 366 0.3 1
Hypersaline (saline) WD272 0 13 1 0.0 0
Hypersaline (saline) Woesearchaeota (DHVEG-6) 71 13 128 0.1 0
Plant corpus Acetothermia 0 123 1 0.0 0
Plant corpus Acidobacteria 95 123 601 0.1 0
Plant corpus Actinobacteria 3284 123 9843 2.5 8
Plant corpus Aerophobetes 1 123 11 0.0 0
Plant corpus Aminicenantes 2 123 10 0.0 0
Plant corpus aquifer1 0 123 1 0.0 0
Plant corpus Aquificae 0 123 0 0.0 0
Plant corpus Armatimonadetes 12 123 43 0.0 0
Plant corpus Atribacteria 2 123 17 0.0 0
Plant corpus Bacteroidetes 1306 123 3687 1.0 3
Plant corpus Candidate division OP3 0 123 1 0.0 0
Plant corpus Candidate division SR1 0 123 1 0.0 0
Plant corpus Chlamydiae 0 123 2 0.0 0
Plant corpus Chlorobi 1 123 4 0.0 0
Plant corpus Chloroflexi 32 123 168 0.0 0
Plant corpus Cyanobacteria 100494 123 61858 77.5 48
Plant corpus Deferribacteres 0 123 3 0.0 0
Plant corpus Deinococcus-Thermus 15 123 77 0.0 0
Plant corpus Elusimicrobia 0 123 1 0.0 0
Plant corpus Euryarchaeota 2 123 11 0.0 0
Plant corpus Fibrobacteres 1 123 4 0.0 0
Plant corpus Firmicutes 1442 123 4930 1.1 4
Plant corpus Fusobacteria 104 123 393 0.1 0
Plant corpus Gemmatimonadetes 15 123 89 0.0 0
Plant corpus Gracilibacteria 0 123 1 0.0 0
Plant corpus Hydrogenedentes 1 123 6 0.0 0
Plant corpus JL-ETNP-Z39 0 123 2 0.0 0
Plant corpus Latescibacteria 0 123 1 0.0 0
Plant corpus Lentisphaerae 0 123 1 0.0 0
Plant corpus Marinimicrobia (SAR406 clade) 0 123 1 0.0 0
Plant corpus Microgenomates 0 123 1 0.0 0
Plant corpus Miscellaneous Crenarchaeotic Group 0 123 1 0.0 0
Plant corpus Nitrospirae 3 123 23 0.0 0
Plant corpus Omnitrophica 0 123 4 0.0 0
Plant corpus Parcubacteria 0 123 0 0.0 0
Plant corpus Planctomycetes 30 123 108 0.0 0
Plant corpus Proteobacteria 22764 123 20513 17.6 16
Plant corpus Saccharibacteria 2 123 8 0.0 0
Plant corpus SHA-109 0 123 1 0.0 0
Plant corpus SM2F11 0 123 0 0.0 0
Plant corpus Spirochaetae 2 123 7 0.0 0
Plant corpus Synergistetes 0 123 3 0.0 0
Plant corpus TA06 0 123 0 0.0 0
Plant corpus Tenericutes 26 123 122 0.0 0
Plant corpus Thaumarchaeota 31 123 202 0.0 0
Plant corpus Thermotogae 0 123 0 0.0 0
Plant corpus TM6 0 123 1 0.0 0
Plant corpus Verrucomicrobia 32 123 104 0.0 0
Plant corpus WCHB1-60 0 123 2 0.0 0
Plant corpus WD272 0 123 0 0.0 0
Plant corpus Woesearchaeota (DHVEG-6) 0 123 0 0.0 0
Plant rhizosphere Acidobacteria 15054 552 13169 14.1 12
Plant rhizosphere Actinobacteria 4532 552 5551 4.2 5
Plant rhizosphere Aenigmarchaeota 4 552 5 0.0 0
Plant rhizosphere Aerophobetes 4 552 5 0.0 0
Plant rhizosphere Aminicenantes 27 552 32 0.0 0
Plant rhizosphere aquifer1 0 552 0 0.0 0
Plant rhizosphere Armatimonadetes 456 552 249 0.4 0
Plant rhizosphere Atribacteria 0 552 0 0.0 0
Plant rhizosphere Bacteroidetes 10383 552 7540 9.7 7
Plant rhizosphere Caldiserica 3 552 5 0.0 0
Plant rhizosphere Candidate division OP3 69 552 68 0.1 0
Plant rhizosphere Candidate division SR1 4 552 6 0.0 0
Plant rhizosphere Candidate division WS6 0 552 0 0.0 0
Plant rhizosphere Chlamydiae 48 552 64 0.0 0
Plant rhizosphere Chlorobi 1307 552 1250 1.2 1
Plant rhizosphere Chloroflexi 4736 552 3491 4.4 3
Plant rhizosphere CKC4 0 552 0 0.0 0
Plant rhizosphere Cloacimonetes 1 552 3 0.0 0
Plant rhizosphere Cyanobacteria 4226 552 4549 4.0 4
Plant rhizosphere Deferribacteres 3 552 9 0.0 0
Plant rhizosphere Deinococcus-Thermus 43 552 48 0.0 0
Plant rhizosphere Diapherotrites 0 552 0 0.0 0
Plant rhizosphere Dictyoglomi 0 552 0 0.0 0
Plant rhizosphere Elusimicrobia 251 552 201 0.2 0
Plant rhizosphere Euryarchaeota 906 552 994 0.8 1
Plant rhizosphere Fibrobacteres 176 552 147 0.2 0
Plant rhizosphere Firmicutes 2173 552 3244 2.0 3
Plant rhizosphere Fusobacteria 5 552 18 0.0 0
Plant rhizosphere GAL08 1 552 2 0.0 0
Plant rhizosphere Gemmatimonadetes 1556 552 2367 1.5 2
Plant rhizosphere GOUTA4 47 552 55 0.0 0
Plant rhizosphere Gracilibacteria 15 552 40 0.0 0
Plant rhizosphere Hydrogenedentes 36 552 24 0.0 0
Plant rhizosphere JL-ETNP-Z39 2 552 13 0.0 0
Plant rhizosphere Kazan-3B-09 0 552 1 0.0 0
Plant rhizosphere Latescibacteria 377 552 290 0.4 0
Plant rhizosphere Lentisphaerae 42 552 43 0.0 0
Plant rhizosphere Marine Hydrothermal Vent Group(MHVG) 0 552 1 0.0 0
Plant rhizosphere Marinimicrobia (SAR406 clade) 1 552 2 0.0 0
Plant rhizosphere Microgenomates 21 552 21 0.0 0
Plant rhizosphere Miscellaneous Crenarchaeotic Group 166 552 205 0.2 0
Plant rhizosphere Miscellaneous Euryarchaeotic Group(MEG) 0 552 1 0.0 0
Plant rhizosphere Nitrospirae 1628 552 1534 1.5 1
Plant rhizosphere OC31 0 552 0 0.0 0
Plant rhizosphere Omnitrophica 56 552 57 0.1 0
Plant rhizosphere Parcubacteria 54 552 58 0.1 0
Plant rhizosphere Parvarchaeota 7 552 12 0.0 0
Plant rhizosphere PAUC34f 2 552 2 0.0 0
Plant rhizosphere Planctomycetes 2599 552 1945 2.4 2
Plant rhizosphere Proteobacteria 48525 552 40482 45.4 38
Plant rhizosphere Saccharibacteria 7 552 13 0.0 0
Plant rhizosphere SHA-109 4 552 6 0.0 0
Plant rhizosphere SM1K20 7 552 10 0.0 0
Plant rhizosphere SM2F11 26 552 25 0.0 0
Plant rhizosphere Spirochaetae 566 552 649 0.5 1
Plant rhizosphere Synergistetes 0 552 1 0.0 0
Plant rhizosphere TA06 45 552 49 0.0 0
Plant rhizosphere Tenericutes 3 552 5 0.0 0
Plant rhizosphere Thaumarchaeota 543 552 1206 0.5 1
Plant rhizosphere Thermotogae 3 552 5 0.0 0
Plant rhizosphere TM6 28 552 64 0.0 0
Plant rhizosphere Verrucomicrobia 6071 552 3839 5.7 4
Plant rhizosphere WCHB1-60 25 552 32 0.0 0
Plant rhizosphere WD272 1 552 4 0.0 0
Plant rhizosphere Woesearchaeota (DHVEG-6) 74 552 85 0.1 0
Plant surface Acidobacteria 300 953 1582 0.4 2
Plant surface Actinobacteria 3281 953 6332 3.9 8
Plant surface Aerophobetes 0 953 1 0.0 0
Plant surface Aminicenantes 0 953 0 0.0 0
Plant surface aquifer1 0 953 0 0.0 0
Plant surface Armatimonadetes 4 953 37 0.0 0
Plant surface Atribacteria 0 953 1 0.0 0
Plant surface Bacteroidetes 13694 953 15776 16.4 19
Plant surface Candidate division OP3 0 953 4 0.0 0
Plant surface Candidate division SR1 0 953 2 0.0 0
Plant surface Chlamydiae 1 953 6 0.0 0
Plant surface Chlorobi 5 953 60 0.0 0
Plant surface Chloroflexi 96 953 538 0.1 1
Plant surface CKC4 0 953 0 0.0 0
Plant surface Cloacimonetes 0 953 0 0.0 0
Plant surface Cyanobacteria 6554 953 11644 7.9 14
Plant surface Deferribacteres 0 953 1 0.0 0
Plant surface Deinococcus-Thermus 67 953 233 0.1 0
Plant surface Elusimicrobia 2 953 16 0.0 0
Plant surface Euryarchaeota 2 953 6 0.0 0
Plant surface Fibrobacteres 1 953 16 0.0 0
Plant surface Firmicutes 223 953 1028 0.3 1
Plant surface Fusobacteria 38 953 129 0.0 0
Plant surface Gemmatimonadetes 57 953 336 0.1 0
Plant surface Gracilibacteria 24 953 52 0.0 0
Plant surface Hyd24-12 0 953 0 0.0 0
Plant surface Hydrogenedentes 0 953 5 0.0 0
Plant surface JL-ETNP-Z39 0 953 0 0.0 0
Plant surface Latescibacteria 9 953 60 0.0 0
Plant surface Lentisphaerae 3 953 11 0.0 0
Plant surface Marinimicrobia (SAR406 clade) 1 953 3 0.0 0
Plant surface Microgenomates 0 953 0 0.0 0
Plant surface Miscellaneous Crenarchaeotic Group 0 953 0 0.0 0
Plant surface Nitrospirae 12 953 68 0.0 0
Plant surface Omnitrophica 0 953 2 0.0 0
Plant surface Parcubacteria 2 953 9 0.0 0
Plant surface PAUC34f 0 953 1 0.0 0
Plant surface Planctomycetes 6198 953 6476 7.4 8
Plant surface Proteobacteria 48527 953 35238 58.2 42
Plant surface RsaHF231 0 953 0 0.0 0
Plant surface Saccharibacteria 0 953 1 0.0 0
Plant surface SHA-109 6 953 27 0.0 0
Plant surface SM2F11 0 953 1 0.0 0
Plant surface Spirochaetae 1 953 4 0.0 0
Plant surface Synergistetes 0 953 0 0.0 0
Plant surface TA06 0 953 0 0.0 0
Plant surface Tenericutes 1 953 14 0.0 0
Plant surface Thaumarchaeota 13 953 95 0.0 0
Plant surface Thermotogae 0 953 0 0.0 0
Plant surface TM6 1 953 5 0.0 0
Plant surface uncultured archaeon 0 1906 0 0.0 0
Plant surface Verrucomicrobia 4280 953 7052 5.1 8
Plant surface WCHB1-60 0 953 2 0.0 0
Plant surface WD272 0 953 1 0.0 0
Plant surface Woesearchaeota (DHVEG-6) 0 953 0 0.0 0
Sediment (non-saline) Acetothermia 2 544 7 0.0 0
Sediment (non-saline) Acidobacteria 5513 544 4427 8.9 7
Sediment (non-saline) Actinobacteria 2577 544 4477 4.2 7
Sediment (non-saline) Aenigmarchaeota 284 544 353 0.5 1
Sediment (non-saline) Aerophobetes 2 544 3 0.0 0
Sediment (non-saline) Aminicenantes 1134 544 1224 1.8 2
Sediment (non-saline) Ancient Archaeal Group(AAG) 0 544 1 0.0 0
Sediment (non-saline) aquifer1 0 544 0 0.0 0
Sediment (non-saline) Aquificae 0 544 0 0.0 0
Sediment (non-saline) Armatimonadetes 146 544 125 0.2 0
Sediment (non-saline) Atribacteria 209 544 621 0.3 1
Sediment (non-saline) Bacteroidetes 3768 544 3871 6.1 6
Sediment (non-saline) Caldiserica 10 544 18 0.0 0
Sediment (non-saline) Candidate division OP3 575 544 528 0.9 1
Sediment (non-saline) Candidate division SR1 4 544 15 0.0 0
Sediment (non-saline) Chlamydiae 8 544 21 0.0 0
Sediment (non-saline) Chlorobi 943 544 766 1.5 1
Sediment (non-saline) Chloroflexi 4979 544 3587 8.0 6
Sediment (non-saline) CKC4 0 544 4 0.0 0
Sediment (non-saline) Cloacimonetes 1 544 6 0.0 0
Sediment (non-saline) Crenarchaeota 120 544 174 0.2 0
Sediment (non-saline) Cyanobacteria 1056 544 2384 1.7 4
Sediment (non-saline) Deferribacteres 67 544 363 0.1 1
Sediment (non-saline) Deinococcus-Thermus 93 544 99 0.2 0
Sediment (non-saline) Diapherotrites 0 544 1 0.0 0
Sediment (non-saline) Dictyoglomi 0 544 0 0.0 0
Sediment (non-saline) Elusimicrobia 121 544 92 0.2 0
Sediment (non-saline) Euryarchaeota 2604 544 2594 4.2 4
Sediment (non-saline) Fibrobacteres 84 544 85 0.1 0
Sediment (non-saline) Firmicutes 590 544 2563 1.0 4
Sediment (non-saline) Fusobacteria 2 544 9 0.0 0
Sediment (non-saline) GAL08 1 544 3 0.0 0
Sediment (non-saline) Gemmatimonadetes 933 544 1378 1.5 2
Sediment (non-saline) GOUTA4 34 544 33 0.1 0
Sediment (non-saline) Gracilibacteria 9 544 16 0.0 0
Sediment (non-saline) Hyd24-12 1 544 5 0.0 0
Sediment (non-saline) Hydrogenedentes 35 544 33 0.1 0
Sediment (non-saline) JL-ETNP-Z39 1 544 7 0.0 0
Sediment (non-saline) Kazan-3B-09 10 544 14 0.0 0
Sediment (non-saline) Latescibacteria 371 544 253 0.6 0
Sediment (non-saline) LCP-89 2 544 4 0.0 0
Sediment (non-saline) LD1-PA38 0 544 1 0.0 0
Sediment (non-saline) Lentisphaerae 130 544 123 0.2 0
Sediment (non-saline) Marine Hydrothermal Vent Group(MHVG) 1 544 1 0.0 0
Sediment (non-saline) Marinimicrobia (SAR406 clade) 3 544 16 0.0 0
Sediment (non-saline) Microgenomates 7 544 9 0.0 0
Sediment (non-saline) Miscellaneous Crenarchaeotic Group 3493 544 5555 5.6 9
Sediment (non-saline) Miscellaneous Euryarchaeotic Group(MEG) 6 544 8 0.0 0
Sediment (non-saline) Nitrospirae 1896 544 1700 3.1 3
Sediment (non-saline) OC31 6 544 22 0.0 0
Sediment (non-saline) Omnitrophica 55 544 69 0.1 0
Sediment (non-saline) Parcubacteria 38 544 35 0.1 0
Sediment (non-saline) Parvarchaeota 1 544 3 0.0 0
Sediment (non-saline) PAUC34f 16 544 18 0.0 0
Sediment (non-saline) Planctomycetes 1524 544 918 2.5 1
Sediment (non-saline) Proteobacteria 24543 544 15795 39.6 25
Sediment (non-saline) Saccharibacteria 1 544 3 0.0 0
Sediment (non-saline) SHA-109 4 544 11 0.0 0
Sediment (non-saline) SM1K20 21 544 25 0.0 0
Sediment (non-saline) SM2F11 5 544 9 0.0 0
Sediment (non-saline) Spirochaetae 316 544 282 0.5 0
Sediment (non-saline) Synergistetes 1 544 7 0.0 0
Sediment (non-saline) TA06 530 544 552 0.9 1
Sediment (non-saline) Tenericutes 3 544 15 0.0 0
Sediment (non-saline) Thaumarchaeota 591 544 819 1.0 1
Sediment (non-saline) Thermotogae 0 544 1 0.0 0
Sediment (non-saline) TM6 19 544 38 0.0 0
Sediment (non-saline) uncultured archaeon 0 1088 0 0.0 0
Sediment (non-saline) Verrucomicrobia 2295 544 2823 3.7 5
Sediment (non-saline) WCHB1-60 5 544 12 0.0 0
Sediment (non-saline) WD272 10 544 58 0.0 0
Sediment (non-saline) Woesearchaeota (DHVEG-6) 145 544 153 0.2 0
Sediment (saline) Acetothermia 5 541 32 0.0 0
Sediment (saline) Acidobacteria 2849 541 6898 2.9 7
Sediment (saline) Actinobacteria 2110 541 2923 2.1 3
Sediment (saline) Aenigmarchaeota 3 541 8 0.0 0
Sediment (saline) Aerophobetes 86 541 1039 0.1 1
Sediment (saline) Aigarchaeota 1 541 2 0.0 0
Sediment (saline) Aminicenantes 190 541 318 0.2 0
Sediment (saline) Ancient Archaeal Group(AAG) 9 541 38 0.0 0
Sediment (saline) aquifer1 5 541 61 0.0 0
Sediment (saline) Aquificae 0 541 0 0.0 0
Sediment (saline) Armatimonadetes 38 541 68 0.0 0
Sediment (saline) Atribacteria 1938 541 28882 1.9 29
Sediment (saline) Bacteroidetes 9904 541 12878 9.9 13
Sediment (saline) Caldiserica 1 541 7 0.0 0
Sediment (saline) Candidate division OP3 145 541 212 0.1 0
Sediment (saline) Candidate division SR1 10 541 41 0.0 0
Sediment (saline) Candidate division WS6 0 541 0 0.0 0
Sediment (saline) Chlamydiae 22 541 40 0.0 0
Sediment (saline) Chlorobi 368 541 748 0.4 1
Sediment (saline) Chloroflexi 2271 541 2829 2.3 3
Sediment (saline) Chrysiogenetes 0 541 0 0.0 0
Sediment (saline) CKC4 0 541 0 0.0 0
Sediment (saline) Cloacimonetes 21 541 70 0.0 0
Sediment (saline) Crenarchaeota 0 541 0 0.0 0
Sediment (saline) Cyanobacteria 1174 541 3824 1.2 4
Sediment (saline) Deferribacteres 251 541 289 0.3 0
Sediment (saline) Deinococcus-Thermus 19 541 97 0.0 0
Sediment (saline) Diapherotrites 0 541 1 0.0 0
Sediment (saline) Dictyoglomi 0 541 0 0.0 0
Sediment (saline) Elusimicrobia 37 541 68 0.0 0
Sediment (saline) Euryarchaeota 579 541 2577 0.6 3
Sediment (saline) Fibrobacteres 71 541 169 0.1 0
Sediment (saline) Firmicutes 1696 541 4052 1.7 4
Sediment (saline) Fusobacteria 92 541 894 0.1 1
Sediment (saline) GAL08 0 541 0 0.0 0
Sediment (saline) Gemmatimonadetes 649 541 684 0.7 1
Sediment (saline) GOUTA4 3 541 9 0.0 0
Sediment (saline) Gracilibacteria 65 541 115 0.1 0
Sediment (saline) Hyd24-12 70 541 140 0.1 0
Sediment (saline) Hydrogenedentes 80 541 107 0.1 0
Sediment (saline) JL-ETNP-Z39 11 541 18 0.0 0
Sediment (saline) Kazan-3B-09 10 541 31 0.0 0
Sediment (saline) Latescibacteria 447 541 458 0.4 0
Sediment (saline) LCP-89 9 541 20 0.0 0
Sediment (saline) LD1-PA38 2 541 5 0.0 0
Sediment (saline) Lentisphaerae 387 541 856 0.4 1
Sediment (saline) Marine Hydrothermal Vent Group(MHVG) 33 541 88 0.0 0
Sediment (saline) Marinimicrobia (SAR406 clade) 131 541 331 0.1 0
Sediment (saline) Microgenomates 12 541 75 0.0 0
Sediment (saline) Miscellaneous Crenarchaeotic Group 79 541 189 0.1 0
Sediment (saline) Miscellaneous Euryarchaeotic Group(MEG) 0 541 0 0.0 0
Sediment (saline) Nanohaloarchaeota 0 541 5 0.0 0
Sediment (saline) Nitrospirae 501 541 638 0.5 1
Sediment (saline) OC31 2 541 6 0.0 0
Sediment (saline) Omnitrophica 55 541 89 0.1 0
Sediment (saline) Parcubacteria 58 541 113 0.1 0
Sediment (saline) Parvarchaeota 0 541 0 0.0 0
Sediment (saline) PAUC34f 37 541 77 0.0 0
Sediment (saline) Planctomycetes 2122 541 2384 2.1 2
Sediment (saline) Proteobacteria 66006 541 49322 66.3 50
Sediment (saline) RsaHF231 0 541 0 0.0 0
Sediment (saline) Saccharibacteria 1 541 10 0.0 0
Sediment (saline) SBYG-2791 0 541 0 0.0 0
Sediment (saline) SHA-109 9 541 29 0.0 0
Sediment (saline) SM1K20 0 541 0 0.0 0
Sediment (saline) SM2F11 1 541 12 0.0 0
Sediment (saline) Spirochaetae 374 541 771 0.4 1
Sediment (saline) Synergistetes 3 541 11 0.0 0
Sediment (saline) TA06 124 541 178 0.1 0
Sediment (saline) Tenericutes 90 541 254 0.1 0
Sediment (saline) Thaumarchaeota 1904 541 3852 1.9 4
Sediment (saline) Thermotogae 1 541 4 0.0 0
Sediment (saline) TM6 43 541 84 0.0 0
Sediment (saline) uncultured archaeon 10 1082 75 0.0 0
Sediment (saline) uncultured bacterium 0 541 2 0.0 0
Sediment (saline) Verrucomicrobia 2251 541 5036 2.3 5
Sediment (saline) WCHB1-60 2 541 8 0.0 0
Sediment (saline) WD272 1 541 20 0.0 0
Sediment (saline) Woesearchaeota (DHVEG-6) 106 541 474 0.1 0
Soil (non-saline) Acetothermia 0 954 0 0.0 0
Soil (non-saline) Acidobacteria 21343 954 22301 20.6 22
Soil (non-saline) Actinobacteria 9428 954 12099 9.1 12
Soil (non-saline) Aenigmarchaeota 0 954 2 0.0 0
Soil (non-saline) Aerophobetes 5 954 11 0.0 0
Soil (non-saline) Aigarchaeota 4 954 88 0.0 0
Soil (non-saline) Aminicenantes 16 954 98 0.0 0
Soil (non-saline) aquifer1 6 954 162 0.0 0
Soil (non-saline) Aquificae 16 954 323 0.0 0
Soil (non-saline) Armatimonadetes 391 954 680 0.4 1
Soil (non-saline) Atribacteria 2 954 15 0.0 0
Soil (non-saline) Bacteroidetes 11108 954 14660 10.7 14
Soil (non-saline) Caldiserica 64 954 467 0.1 0
Soil (non-saline) Candidate division OP3 42 954 152 0.0 0
Soil (non-saline) Candidate division SR1 5 954 23 0.0 0
Soil (non-saline) Candidate division WS6 0 954 0 0.0 0
Soil (non-saline) Chlamydiae 67 954 153 0.1 0
Soil (non-saline) Chlorobi 365 954 1038 0.4 1
Soil (non-saline) Chloroflexi 2393 954 3026 2.3 3
Soil (non-saline) CKC4 0 954 0 0.0 0
Soil (non-saline) Cloacimonetes 1 954 10 0.0 0
Soil (non-saline) Crenarchaeota 18 954 360 0.0 0
Soil (non-saline) Cyanobacteria 630 954 2090 0.6 2
Soil (non-saline) Deferribacteres 1 954 5 0.0 0
Soil (non-saline) Deinococcus-Thermus 24 954 103 0.0 0
Soil (non-saline) Diapherotrites 0 954 0 0.0 0
Soil (non-saline) Dictyoglomi 0 954 0 0.0 0
Soil (non-saline) Elusimicrobia 215 954 281 0.2 0
Soil (non-saline) Euryarchaeota 193 954 656 0.2 1
Soil (non-saline) Fibrobacteres 78 954 299 0.1 0
Soil (non-saline) Firmicutes 4339 954 12302 4.2 12
Soil (non-saline) Fusobacteria 28 954 288 0.0 0
Soil (non-saline) GAL08 0 954 1 0.0 0
Soil (non-saline) Gemmatimonadetes 2564 954 3689 2.5 4
Soil (non-saline) GOUTA4 4 954 23 0.0 0
Soil (non-saline) Gracilibacteria 3 954 14 0.0 0
Soil (non-saline) Hyd24-12 0 954 0 0.0 0
Soil (non-saline) Hydrogenedentes 19 954 39 0.0 0
Soil (non-saline) JL-ETNP-Z39 21 954 116 0.0 0
Soil (non-saline) Kazan-3B-09 0 954 0 0.0 0
Soil (non-saline) Latescibacteria 234 954 474 0.2 0
Soil (non-saline) LCP-89 0 954 0 0.0 0
Soil (non-saline) Lentisphaerae 32 954 89 0.0 0
Soil (non-saline) Marine Hydrothermal Vent Group(MHVG) 0 954 0 0.0 0
Soil (non-saline) Marinimicrobia (SAR406 clade) 1 954 13 0.0 0
Soil (non-saline) Microgenomates 23 954 110 0.0 0
Soil (non-saline) Miscellaneous Crenarchaeotic Group 80 954 1010 0.1 1
Soil (non-saline) Miscellaneous Euryarchaeotic Group(MEG) 0 954 0 0.0 0
Soil (non-saline) Nitrospirae 984 954 1565 0.9 2
Soil (non-saline) OC31 0 954 0 0.0 0
Soil (non-saline) Omnitrophica 20 954 61 0.0 0
Soil (non-saline) Parcubacteria 35 954 98 0.0 0
Soil (non-saline) Parvarchaeota 0 954 2 0.0 0
Soil (non-saline) PAUC34f 0 954 3 0.0 0
Soil (non-saline) Planctomycetes 1987 954 2464 1.9 2
Soil (non-saline) Proteobacteria 34608 954 28725 33.4 28
Soil (non-saline) RsaHF231 0 954 0 0.0 0
Soil (non-saline) Saccharibacteria 10 954 21 0.0 0
Soil (non-saline) SHA-109 7 954 14 0.0 0
Soil (non-saline) SM1K20 0 954 3 0.0 0
Soil (non-saline) SM2F11 27 954 64 0.0 0
Soil (non-saline) Spirochaetae 61 954 265 0.1 0
Soil (non-saline) Synergistetes 0 954 2 0.0 0
Soil (non-saline) TA06 10 954 55 0.0 0
Soil (non-saline) Tenericutes 34 954 615 0.0 1
Soil (non-saline) Thaumarchaeota 816 954 2454 0.8 2
Soil (non-saline) Thermotogae 5 954 51 0.0 0
Soil (non-saline) TM6 47 954 99 0.0 0
Soil (non-saline) uncultured archaeon 2 1908 33 0.0 0
Soil (non-saline) Verrucomicrobia 10922 954 12722 10.5 12
Soil (non-saline) WCHB1-60 39 954 84 0.0 0
Soil (non-saline) WD272 240 954 1304 0.2 1
Soil (non-saline) Woesearchaeota (DHVEG-6) 10 954 55 0.0 0
Surface (non-saline) Acetothermia 3 953 55 0.0 0
Surface (non-saline) Acidobacteria 1638 953 4822 2.8 8
Surface (non-saline) Actinobacteria 7052 953 9451 12.2 16
Surface (non-saline) Aenigmarchaeota 0 953 0 0.0 0
Surface (non-saline) Aerophobetes 1 953 4 0.0 0
Surface (non-saline) Aigarchaeota 3 953 31 0.0 0
Surface (non-saline) Aminicenantes 2 953 20 0.0 0
Surface (non-saline) aquifer1 3 953 15 0.0 0
Surface (non-saline) Aquificae 286 953 988 0.5 2
Surface (non-saline) Armatimonadetes 451 953 739 0.8 1
Surface (non-saline) Atribacteria 1 953 10 0.0 0
Surface (non-saline) Bacteroidetes 3868 953 5950 6.7 10
Surface (non-saline) Caldiserica 1 953 20 0.0 0
Surface (non-saline) Calescamantes 0 953 3 0.0 0
Surface (non-saline) Candidate division OP3 5 953 31 0.0 0
Surface (non-saline) Candidate division SR1 18 953 128 0.0 0
Surface (non-saline) Candidate division WS6 0 953 0 0.0 0
Surface (non-saline) Chlamydiae 27 953 219 0.0 0
Surface (non-saline) Chlorobi 332 953 635 0.6 1
Surface (non-saline) Chloroflexi 875 953 1584 1.5 3
Surface (non-saline) Chrysiogenetes 0 953 0 0.0 0
Surface (non-saline) CKC4 0 953 1 0.0 0
Surface (non-saline) Cloacimonetes 0 953 3 0.0 0
Surface (non-saline) Crenarchaeota 1 953 6 0.0 0
Surface (non-saline) Cyanobacteria 4064 953 5189 7.0 9
Surface (non-saline) Deferribacteres 1 953 16 0.0 0
Surface (non-saline) Deinococcus-Thermus 364 953 757 0.6 1
Surface (non-saline) Diapherotrites 0 953 3 0.0 0
Surface (non-saline) Dictyoglomi 0 953 0 0.0 0
Surface (non-saline) Elusimicrobia 9 953 47 0.0 0
Surface (non-saline) Euryarchaeota 12 953 67 0.0 0
Surface (non-saline) Fibrobacteres 3 953 14 0.0 0
Surface (non-saline) Firmicutes 11291 953 16134 19.5 28
Surface (non-saline) Fusobacteria 230 953 706 0.4 1
Surface (non-saline) GAL08 0 953 3 0.0 0
Surface (non-saline) Gemmatimonadetes 248 953 736 0.4 1
Surface (non-saline) GOUTA4 0 953 3 0.0 0
Surface (non-saline) Gracilibacteria 8 953 62 0.0 0
Surface (non-saline) Hyd24-12 0 953 1 0.0 0
Surface (non-saline) Hydrogenedentes 4 953 33 0.0 0
Surface (non-saline) JL-ETNP-Z39 0 953 3 0.0 0
Surface (non-saline) Kazan-3B-09 0 953 0 0.0 0
Surface (non-saline) Latescibacteria 32 953 298 0.1 1
Surface (non-saline) LCP-89 0 953 1 0.0 0
Surface (non-saline) Lentisphaerae 10 953 37 0.0 0
Surface (non-saline) Marinimicrobia (SAR406 clade) 0 953 4 0.0 0
Surface (non-saline) Microgenomates 2 953 14 0.0 0
Surface (non-saline) Miscellaneous Crenarchaeotic Group 1 953 14 0.0 0
Surface (non-saline) Miscellaneous Euryarchaeotic Group(MEG) 6 953 22 0.0 0
Surface (non-saline) Nanoarchaeota 0 953 0 0.0 0
Surface (non-saline) Nitrospirae 222 953 1966 0.4 3
Surface (non-saline) OC31 0 953 0 0.0 0
Surface (non-saline) Omnitrophica 3 953 26 0.0 0
Surface (non-saline) Parcubacteria 10 953 38 0.0 0
Surface (non-saline) Parvarchaeota 0 953 0 0.0 0
Surface (non-saline) PAUC34f 0 953 5 0.0 0
Surface (non-saline) Planctomycetes 445 953 1198 0.8 2
Surface (non-saline) Proteobacteria 21389 953 25991 37.0 45
Surface (non-saline) RsaHF231 0 953 2 0.0 0
Surface (non-saline) S2R-29 19 953 55 0.0 0
Surface (non-saline) Saccharibacteria 3 953 12 0.0 0
Surface (non-saline) SHA-109 3 953 9 0.0 0
Surface (non-saline) SM1K20 0 953 0 0.0 0
Surface (non-saline) SM2F11 4 953 24 0.0 0
Surface (non-saline) Spirochaetae 15 953 47 0.0 0
Surface (non-saline) Synergistetes 1 953 7 0.0 0
Surface (non-saline) TA06 6 953 56 0.0 0
Surface (non-saline) Tenericutes 3885 953 7795 6.7 13
Surface (non-saline) Thaumarchaeota 62 953 543 0.1 1
Surface (non-saline) Thermodesulfobacteria 0 953 2 0.0 0
Surface (non-saline) Thermotogae 140 953 310 0.2 1
Surface (non-saline) TM6 9 953 55 0.0 0
Surface (non-saline) uncultured archaeon 0 1906 0 0.0 0
Surface (non-saline) Verrucomicrobia 749 953 1918 1.3 3
Surface (non-saline) WCHB1-60 2 953 9 0.0 0
Surface (non-saline) WD272 1 953 4 0.0 0
Surface (non-saline) Woesearchaeota (DHVEG-6) 1 953 12 0.0 0
Surface (saline) Acetothermia 71 117 378 0.0 0
Surface (saline) Acidobacteria 1374 117 3427 0.9 2
Surface (saline) Actinobacteria 5011 117 7693 3.3 5
Surface (saline) Aenigmarchaeota 0 117 1 0.0 0
Surface (saline) Aerophobetes 4 117 10 0.0 0
Surface (saline) Aminicenantes 12 117 37 0.0 0
Surface (saline) Ancient Archaeal Group(AAG) 0 117 0 0.0 0
Surface (saline) aquifer1 0 117 3 0.0 0
Surface (saline) Aquificae 108 117 963 0.1 1
Surface (saline) Armatimonadetes 124 117 398 0.1 0
Surface (saline) Atribacteria 30 117 169 0.0 0
Surface (saline) Bacteroidetes 20892 117 17969 13.7 12
Surface (saline) Caldiserica 0 117 1 0.0 0
Surface (saline) Candidate division OP3 55 117 304 0.0 0
Surface (saline) Candidate division SR1 13 117 46 0.0 0
Surface (saline) Chlamydiae 8 117 22 0.0 0
Surface (saline) Chlorobi 181 117 384 0.1 0
Surface (saline) Chloroflexi 820 117 1807 0.5 1
Surface (saline) CKC4 0 117 0 0.0 0
Surface (saline) Cloacimonetes 6 117 24 0.0 0
Surface (saline) Cyanobacteria 22891 117 43067 15.0 28
Surface (saline) Deferribacteres 105 117 438 0.1 0
Surface (saline) Deinococcus-Thermus 44 117 174 0.0 0
Surface (saline) Diapherotrites 0 117 0 0.0 0
Surface (saline) Dictyoglomi 0 117 1 0.0 0
Surface (saline) Elusimicrobia 17 117 54 0.0 0
Surface (saline) Euryarchaeota 110 117 271 0.1 0
Surface (saline) Fibrobacteres 25 117 71 0.0 0
Surface (saline) Firmicutes 10261 117 23703 6.7 16
Surface (saline) Fusobacteria 190 117 1620 0.1 1
Surface (saline) Gemmatimonadetes 267 117 642 0.2 0
Surface (saline) GOUTA4 0 117 2 0.0 0
Surface (saline) Gracilibacteria 104 117 358 0.1 0
Surface (saline) Hyd24-12 4 117 14 0.0 0
Surface (saline) Hydrogenedentes 18 117 44 0.0 0
Surface (saline) JL-ETNP-Z39 2 117 10 0.0 0
Surface (saline) Kazan-3B-09 1 117 3 0.0 0
Surface (saline) Latescibacteria 112 117 287 0.1 0
Surface (saline) LCP-89 0 117 2 0.0 0
Surface (saline) LD1-PA38 1 117 3 0.0 0
Surface (saline) Lentisphaerae 255 117 724 0.2 0
Surface (saline) Marine Hydrothermal Vent Group(MHVG) 0 117 1 0.0 0
Surface (saline) Marinimicrobia (SAR406 clade) 43 117 138 0.0 0
Surface (saline) Microgenomates 2 117 12 0.0 0
Surface (saline) Miscellaneous Crenarchaeotic Group 4 117 15 0.0 0
Surface (saline) Miscellaneous Euryarchaeotic Group(MEG) 0 117 0 0.0 0
Surface (saline) Nitrospirae 1321 117 5461 0.9 4
Surface (saline) OC31 0 117 2 0.0 0
Surface (saline) Omnitrophica 277 117 829 0.2 1
Surface (saline) Parcubacteria 60 117 130 0.0 0
Surface (saline) Parvarchaeota 0 117 1 0.0 0
Surface (saline) PAUC34f 11 117 61 0.0 0
Surface (saline) Planctomycetes 3328 117 6570 2.2 4
Surface (saline) Proteobacteria 80232 117 46373 52.5 30
Surface (saline) RsaHF231 0 117 0 0.0 0
Surface (saline) Saccharibacteria 2 117 4 0.0 0
Surface (saline) SHA-109 16 117 40 0.0 0
Surface (saline) SM1K20 0 117 0 0.0 0
Surface (saline) SM2F11 4 117 23 0.0 0
Surface (saline) Spirochaetae 101 117 272 0.1 0
Surface (saline) Synergistetes 3 117 16 0.0 0
Surface (saline) TA06 8 117 24 0.0 0
Surface (saline) Tenericutes 33 117 154 0.0 0
Surface (saline) Thaumarchaeota 292 117 847 0.2 1
Surface (saline) Thermotogae 1 117 6 0.0 0
Surface (saline) TM6 25 117 53 0.0 0
Surface (saline) uncultured archaeon 1 234 6 0.0 0
Surface (saline) Verrucomicrobia 3967 117 6640 2.6 4
Surface (saline) WCHB1-60 14 117 47 0.0 0
Surface (saline) WD272 0 117 1 0.0 0
Surface (saline) Woesearchaeota (DHVEG-6) 53 117 134 0.0 0
Water (non-saline) Acetothermia 1 954 4 0.0 0
Water (non-saline) Acidobacteria 1590 954 4700 1.2 3
Water (non-saline) Actinobacteria 24041 954 51850 17.9 39
Water (non-saline) Aenigmarchaeota 1 954 3 0.0 0
Water (non-saline) Aerophobetes 1 954 5 0.0 0
Water (non-saline) Aminicenantes 41 954 279 0.0 0
Water (non-saline) aquifer1 1 954 8 0.0 0
Water (non-saline) Aquificae 0 954 0 0.0 0
Water (non-saline) Armatimonadetes 229 954 1351 0.2 1
Water (non-saline) Atribacteria 2 954 17 0.0 0
Water (non-saline) Bacteroidetes 26067 954 50661 19.4 38
Water (non-saline) Caldiserica 1 954 8 0.0 0
Water (non-saline) Candidate division OP3 161 954 423 0.1 0
Water (non-saline) Candidate division SR1 17 954 45 0.0 0
Water (non-saline) Candidate division WS6 0 954 0 0.0 0
Water (non-saline) Chlamydiae 104 954 1488 0.1 1
Water (non-saline) Chlorobi 785 954 2952 0.6 2
Water (non-saline) Chloroflexi 1471 954 3662 1.1 3
Water (non-saline) CKC4 0 954 6 0.0 0
Water (non-saline) Cloacimonetes 3 954 21 0.0 0
Water (non-saline) Crenarchaeota 1 954 5 0.0 0
Water (non-saline) Cyanobacteria 14013 954 33077 10.4 25
Water (non-saline) Deferribacteres 3 954 38 0.0 0
Water (non-saline) Deinococcus-Thermus 19 954 74 0.0 0
Water (non-saline) Diapherotrites 0 954 2 0.0 0
Water (non-saline) Dictyoglomi 0 954 0 0.0 0
Water (non-saline) Elusimicrobia 128 954 465 0.1 0
Water (non-saline) Euryarchaeota 99 954 496 0.1 0
Water (non-saline) Fibrobacteres 39 954 120 0.0 0
Water (non-saline) Firmicutes 1851 954 10266 1.4 8
Water (non-saline) Fusobacteria 25 954 188 0.0 0
Water (non-saline) GAL08 0 954 2 0.0 0
Water (non-saline) Gemmatimonadetes 332 954 1244 0.2 1
Water (non-saline) GOUTA4 1 954 8 0.0 0
Water (non-saline) Gracilibacteria 23 954 63 0.0 0
Water (non-saline) Hyd24-12 1 954 6 0.0 0
Water (non-saline) Hydrogenedentes 4 954 14 0.0 0
Water (non-saline) JL-ETNP-Z39 0 954 1 0.0 0
Water (non-saline) Kazan-3B-09 1 954 5 0.0 0
Water (non-saline) Latescibacteria 49 954 152 0.0 0
Water (non-saline) LCP-89 0 954 3 0.0 0
Water (non-saline) Lentisphaerae 89 954 517 0.1 0
Water (non-saline) Marine Hydrothermal Vent Group(MHVG) 0 954 0 0.0 0
Water (non-saline) Marinimicrobia (SAR406 clade) 10 954 88 0.0 0
Water (non-saline) Microgenomates 17 954 50 0.0 0
Water (non-saline) Miscellaneous Crenarchaeotic Group 33 954 241 0.0 0
Water (non-saline) Miscellaneous Euryarchaeotic Group(MEG) 0 954 2 0.0 0
Water (non-saline) Nitrospirae 195 954 563 0.1 0
Water (non-saline) OC31 0 954 4 0.0 0
Water (non-saline) Omnitrophica 77 954 220 0.1 0
Water (non-saline) Parcubacteria 242 954 1059 0.2 1
Water (non-saline) Parvarchaeota 2 954 8 0.0 0
Water (non-saline) PAUC34f 2 954 10 0.0 0
Water (non-saline) Planctomycetes 2245 954 3986 1.7 3
Water (non-saline) Proteobacteria 54265 954 86306 40.3 64
Water (non-saline) RsaHF231 1 954 6 0.0 0
Water (non-saline) Saccharibacteria 44 954 132 0.0 0
Water (non-saline) SHA-109 3 954 10 0.0 0
Water (non-saline) SM1K20 2 954 11 0.0 0
Water (non-saline) SM2F11 45 954 161 0.0 0
Water (non-saline) Spirochaetae 50 954 207 0.0 0
Water (non-saline) Synergistetes 3 954 37 0.0 0
Water (non-saline) TA06 8 954 31 0.0 0
Water (non-saline) Tenericutes 8 954 54 0.0 0
Water (non-saline) Thaumarchaeota 74 954 308 0.1 0
Water (non-saline) Thermotogae 1 954 5 0.0 0
Water (non-saline) TM6 49 954 180 0.0 0
Water (non-saline) uncultured archaeon 0 1908 1 0.0 0
Water (non-saline) Verrucomicrobia 5904 954 12303 4.4 9
Water (non-saline) WCHB1-60 44 954 124 0.0 0
Water (non-saline) WD272 1 954 7 0.0 0
Water (non-saline) Woesearchaeota (DHVEG-6) 26 954 80 0.0 0
Water (saline) Acetothermia 0 682 6 0.0 0
Water (saline) Acidobacteria 708 682 9258 0.4 5
Water (saline) Actinobacteria 4280 682 8209 2.5 5
Water (saline) Aenigmarchaeota 0 682 0 0.0 0
Water (saline) Aerophobetes 3 682 34 0.0 0
Water (saline) Aigarchaeota 0 682 1 0.0 0
Water (saline) Aminicenantes 3 682 30 0.0 0
Water (saline) Ancient Archaeal Group(AAG) 0 682 0 0.0 0
Water (saline) aquifer1 0 682 1 0.0 0
Water (saline) Aquificae 0 682 0 0.0 0
Water (saline) Armatimonadetes 3 682 20 0.0 0
Water (saline) Atribacteria 1 682 20 0.0 0
Water (saline) Bacteroidetes 49447 682 67127 28.8 39
Water (saline) Caldiserica 0 682 6 0.0 0
Water (saline) Candidate division OP3 11 682 85 0.0 0
Water (saline) Candidate division SR1 0 682 2 0.0 0
Water (saline) Chlamydiae 3 682 18 0.0 0
Water (saline) Chlorobi 32 682 352 0.0 0
Water (saline) Chloroflexi 496 682 1814 0.3 1
Water (saline) CKC4 0 682 1 0.0 0
Water (saline) Cloacimonetes 12 682 158 0.0 0
Water (saline) Crenarchaeota 0 682 2 0.0 0
Water (saline) Cyanobacteria 21919 682 50275 12.8 29
Water (saline) Deferribacteres 7 682 85 0.0 0
Water (saline) Deinococcus-Thermus 2 682 14 0.0 0
Water (saline) Diapherotrites 0 682 0 0.0 0
Water (saline) Dictyoglomi 0 682 0 0.0 0
Water (saline) Elusimicrobia 2 682 11 0.0 0
Water (saline) Euryarchaeota 840 682 2879 0.5 2
Water (saline) Fibrobacteres 8 682 54 0.0 0
Water (saline) Firmicutes 210 682 986 0.1 1
Water (saline) Fusobacteria 62 682 1043 0.0 1
Water (saline) GAL08 0 682 0 0.0 0
Water (saline) Gemmatimonadetes 100 682 379 0.1 0
Water (saline) GOUTA4 0 682 2 0.0 0
Water (saline) Gracilibacteria 26 682 48 0.0 0
Water (saline) Hyd24-12 3 682 62 0.0 0
Water (saline) Hydrogenedentes 1 682 9 0.0 0
Water (saline) JL-ETNP-Z39 2 682 22 0.0 0
Water (saline) Kazan-3B-09 1 682 13 0.0 0
Water (saline) Latescibacteria 9 682 74 0.0 0
Water (saline) LCP-89 1 682 9 0.0 0
Water (saline) LD1-PA38 0 682 0 0.0 0
Water (saline) Lentisphaerae 18 682 102 0.0 0
Water (saline) Marine Hydrothermal Vent Group(MHVG) 0 682 1 0.0 0
Water (saline) Marinimicrobia (SAR406 clade) 3425 682 9294 2.0 5
Water (saline) Microgenomates 0 682 2 0.0 0
Water (saline) Miscellaneous Crenarchaeotic Group 2 682 35 0.0 0
Water (saline) Miscellaneous Euryarchaeotic Group(MEG) 0 682 1 0.0 0
Water (saline) Nitrospirae 57 682 270 0.0 0
Water (saline) OC31 0 682 1 0.0 0
Water (saline) Omnitrophica 2 682 12 0.0 0
Water (saline) Parcubacteria 7 682 37 0.0 0
Water (saline) Parvarchaeota 0 682 0 0.0 0
Water (saline) PAUC34f 52 682 221 0.0 0
Water (saline) Planctomycetes 949 682 3828 0.6 2
Water (saline) Proteobacteria 86484 682 90270 50.4 53
Water (saline) RsaHF231 0 682 0 0.0 0
Water (saline) Saccharibacteria 18 682 191 0.0 0
Water (saline) SBYG-2791 0 682 1 0.0 0
Water (saline) SHA-109 1 682 8 0.0 0
Water (saline) SM1K20 0 682 1 0.0 0
Water (saline) SM2F11 0 682 1 0.0 0
Water (saline) Spirochaetae 25 682 412 0.0 0
Water (saline) Synergistetes 0 682 2 0.0 0
Water (saline) TA06 4 682 61 0.0 0
Water (saline) Tenericutes 5 682 33 0.0 0
Water (saline) Thaumarchaeota 1250 682 5228 0.7 3
Water (saline) Thermotogae 0 682 1 0.0 0
Water (saline) TM6 4 682 22 0.0 0
Water (saline) uncultured archaeon 0 1364 0 0.0 0
Water (saline) Verrucomicrobia 1230 682 5687 0.7 3
Water (saline) WCHB1-60 0 682 1 0.0 0
Water (saline) WD272 0 682 5 0.0 0
Water (saline) Woesearchaeota (DHVEG-6) 3 682 25 0.0 0
# save summary table
taxa_sum_df %>% 
  filter(`Abundance (mean)` != 0) %>% 
  write.csv(file = paste0("EMP_", Grouping_var,"_", Rank,".csv"))

Plot heatmaps

# Agglomerate taxa
EMP %>% 
  tax_glom(Rank, NArm = TRUE) %>% 
  transform_sample_counts(function(x) x / sum(x) * 100) ->
  Ps_obj_filt_glom

plot_heatmap(
  Ps_obj_filt_glom,
  # method = "NMDS",
  # distance = "bray",
  trans = log_trans(4),
  sample.order = Grouping_var,
  sample.label = Grouping_var,
  taxa.label = Rank,
  taxa.order = Rank_order$OTU
) + 
  theme_bw(base_size = 18) + 
  theme(axis.text.x = element_text(angle = 45.0, vjust = 1, hjust = 1)) +
  scale_fill_viridis(trans = "log", labels = scales::number_format(accuracy = 0.1), option = "magma", na.value = "black") +
  labs(fill = "Abundance (%)")

# Agglomerate taxa
EMP_merge %>% 
  tax_glom(Rank, NArm = TRUE) %>% 
  transform_sample_counts(function(x) x / sum(x) * 100) ->
  Ps_obj_filt_glom

plot_heatmap(
  Ps_obj_filt_glom,
  # method = "NMDS",
  # distance = "bray",
  trans = log_trans(4),
  sample.order = Grouping_var,
  sample.label = Grouping_var,
  taxa.label = Rank,
  taxa.order = Rank_order$OTU
) + 
  theme_bw(base_size = 18) + 
  theme(axis.text.x = element_text(angle = 45.0, vjust = 1, hjust = 1)) +
  scale_fill_viridis(trans = "log", labels = scales::number_format(accuracy = 0.1), option = "magma", na.value = "black") +
  labs(fill = "Abundance (%)")

Plot a bar chart

EMP_merge %>% 
  tax_glom(., Rank) %>% 
  transform_sample_counts(., function(x) x / sum(x) * 100) %>% 
  psmelt() %>%  
  mutate_if(is.character, as.factor) %>% 
  mutate(Phylum = fct_relevel(pull(., Rank), rev(unique(pull(Rank_order, Rank))))) %>% 
  ggplot(aes(fill = !!sym(Rank), x = !!sym(Grouping_var), y = log10(Abundance))) +
  geom_col() +
  theme_set(theme_bw()) +
  theme(axis.text.x = element_text(angle = 45.0, vjust = 1, hjust = 1),
        legend.position = "bottom") +
  labs(y = "Log10 rel. abundance") +
  facet_wrap(~get(Rank), ncol = 5) +
  theme(legend.position = "none")

Plot a violin and dot chart

EMP %>% 
  tax_glom(., Rank) %>% 
  transform_sample_counts(., function(x) x / sum(x) * 100) %>% 
  psmelt() %>%  
  mutate_if(is.character, as.factor) %>% 
  mutate(Taxa = fct_relevel(pull(., Rank), rev(unique(pull(Rank_order, Rank))))) %>%
  mutate(Taxa = fct_other(Taxa, drop = pull(Rank_order, Rank)[Rank_order$`Abundance (mean)` < 0.1], other_level = "Rare")) %>% 
  ggplot(aes(x = Taxa, y = Abundance)) +
  geom_violin(aes(group = interaction(Taxa, !!sym(Grouping_var))),
              scale = "width") +
  geom_point2(aes(colour = Taxa), 
              position = position_jitter(width = 0.2),
             alpha = 1/4,
             stroke = 0, 
             size = 2) +
  theme(axis.text = element_text(angle = 45.0), 
        axis.text.x = element_text(vjust = 1, hjust = 1) ) + 
  # scale_fill_locuszoom() +
  # scale_color_manual(values = pal("d3js")[c(3, 4, 2)]) +
  labs(x = NULL, y = "Abundance (%)", colour = Rank) + 
  guides(colour = guide_legend(override.aes = list(size = 5, alpha = 1))) + 
  facet_wrap(~get(Grouping_var), ncol = 2)  +
  theme(legend.position = "none")

Generate heat-tree plots using Metacoder (Foster, Sharpton, and Grünwald 2017)

# Convert phyloseq to taxmap
EMP %>% 
  # transform_sample_counts(function(x) x / sum(x) ) %>% # not really needed
  parse_phyloseq() %>% 
  filter_taxa(., !taxon_ranks %in% c("Species", "Genus", "Family", "Order")) -> # tips will be Class
  EMP_taxmap

# Potentially drop out low reads
# EMP_taxmap$data$otu_table <- zero_low_counts(EMP_taxmap, "otu_table", min_count = 5)
# no_reads <- rowSums(EMP_taxmap$data$otu_table[, EMP_taxmap$data$sample_data$sample_id]) == 0
# EMP_taxmap <- filter_obs(EMP_taxmap, data = "tax_data", ! no_reads, drop_taxa = TRUE)

# Sum counts per group
EMP_taxmap$data$tax_counts <- calc_taxon_abund(EMP_taxmap, 
                                                      data = 'otu_table', 
                                                      cols = EMP_taxmap$data$sample_data$sample_id, 
                                                      groups = pull(EMP_taxmap$data$sample_data, Grouping_var))

# Generate a plot for each group
my_plots <- lapply(sort(unique(get_variable(EMP, Grouping_var))), function(group) {
  # do something with time point data
  set.seed(2020) # Make each plot layout look the same if using another layout
  EMP_taxmap %>% 
    heat_tree(.,
              node_label = taxon_names,
              node_size = n_obs,
              node_color = EMP_taxmap$data$tax_counts[[group]],
              node_size_axis_label = 'OTU count',
              node_color_axis_label = 'Sequence count',
              layout = "automatic",
              node_size_range = c(0.013, 0.04), 
              title = group)
})

wrap_plots(my_plots, ncol = 3)

Colophon

sessioninfo::session_info() %>%
  details::details(
    summary = 'Current session info',
    open    = TRUE
  )
Current session info
─ Session info ─────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.1.0 (2021-05-18)
 os       Ubuntu 18.04.5 LTS          
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       Europe/Prague               
 date     2021-07-23                  

─ Packages ─────────────────────────────────────────────────────────────────────────────
 package          * version    date       lib source                                
 ade4               1.7-17     2021-06-17 [1] CRAN (R 4.1.0)                        
 ape                5.5        2021-04-25 [1] CRAN (R 4.0.3)                        
 assertthat         0.2.1      2019-03-21 [1] CRAN (R 4.0.2)                        
 backports          1.2.1      2020-12-09 [1] CRAN (R 4.0.2)                        
 bayestestR         0.10.0     2021-05-31 [1] CRAN (R 4.1.0)                        
 Biobase            2.52.0     2021-05-19 [1] Bioconductor                          
 BiocGenerics       0.38.0     2021-05-19 [1] Bioconductor                          
 biomformat         1.20.0     2021-05-19 [1] Bioconductor                          
 Biostrings         2.60.1     2021-06-06 [1] Bioconductor                          
 bit                4.0.4      2020-08-04 [1] CRAN (R 4.0.2)                        
 bit64              4.0.5      2020-08-30 [1] CRAN (R 4.0.2)                        
 bitops             1.0-7      2021-04-24 [1] CRAN (R 4.0.3)                        
 broom              0.7.8      2021-06-24 [1] CRAN (R 4.1.0)                        
 cellranger         1.1.0      2016-07-27 [1] CRAN (R 4.0.2)                        
 cli                3.0.1      2021-07-17 [1] CRAN (R 4.1.0)                        
 clipr              0.7.1      2020-10-08 [1] CRAN (R 4.0.2)                        
 cluster            2.1.2      2021-04-17 [1] CRAN (R 4.0.3)                        
 coda               0.19-4     2020-09-30 [1] CRAN (R 4.0.2)                        
 codetools          0.2-18     2020-11-04 [1] CRAN (R 4.0.2)                        
 colorspace         2.0-2      2021-06-24 [1] CRAN (R 4.1.0)                        
 crayon             1.4.1      2021-02-08 [1] CRAN (R 4.0.3)                        
 data.table         1.14.0     2021-02-21 [1] CRAN (R 4.0.3)                        
 DBI                1.1.1      2021-01-15 [1] CRAN (R 4.0.3)                        
 dbplyr             2.1.1      2021-04-06 [1] CRAN (R 4.0.3)                        
 desc               1.3.0      2021-03-05 [1] CRAN (R 4.0.3)                        
 details            0.2.1      2020-01-12 [1] CRAN (R 4.0.2)                        
 digest             0.6.27     2020-10-24 [1] CRAN (R 4.0.2)                        
 dplyr            * 1.0.7      2021-06-18 [1] CRAN (R 4.1.0)                        
 effectsize         0.4.5      2021-05-25 [1] CRAN (R 4.1.0)                        
 ellipsis           0.3.2      2021-04-29 [1] CRAN (R 4.0.3)                        
 emmeans            1.6.2-1    2021-07-08 [1] CRAN (R 4.1.0)                        
 estimability       1.3        2018-02-11 [1] CRAN (R 4.0.2)                        
 evaluate           0.14       2019-05-28 [1] CRAN (R 4.0.2)                        
 extrafont        * 0.17       2014-12-08 [1] CRAN (R 4.1.0)                        
 extrafontdb        1.0        2012-06-11 [1] CRAN (R 4.0.2)                        
 fansi              0.5.0      2021-05-25 [1] CRAN (R 4.0.3)                        
 farver             2.1.0      2021-02-28 [1] CRAN (R 4.0.3)                        
 forcats          * 0.5.1      2021-01-27 [1] CRAN (R 4.0.3)                        
 foreach            1.5.1      2020-10-15 [1] CRAN (R 4.0.2)                        
 fs                 1.5.0      2020-07-31 [1] CRAN (R 4.0.2)                        
 generics           0.1.0      2020-10-31 [1] CRAN (R 4.0.2)                        
 GenomeInfoDb       1.28.1     2021-07-01 [1] Bioconductor                          
 GenomeInfoDbData   1.2.6      2021-05-25 [1] Bioconductor                          
 ggfittext          0.9.1      2021-01-30 [1] CRAN (R 4.0.3)                        
 ggplot2          * 3.3.5      2021-06-25 [1] CRAN (R 4.1.0)                        
 ggridges           0.5.3      2021-01-08 [1] CRAN (R 4.0.2)                        
 ggtext           * 0.1.1      2020-12-17 [1] CRAN (R 4.0.2)                        
 glue               1.4.2      2020-08-27 [1] CRAN (R 4.0.2)                        
 gridExtra          2.3        2017-09-09 [1] CRAN (R 4.0.2)                        
 gridtext           0.1.4      2020-12-10 [1] CRAN (R 4.0.2)                        
 gtable             0.3.0      2019-03-25 [1] CRAN (R 4.0.2)                        
 haven              2.4.1      2021-04-23 [1] CRAN (R 4.0.3)                        
 highr              0.9        2021-04-16 [1] CRAN (R 4.0.3)                        
 hms                1.1.0      2021-05-17 [1] CRAN (R 4.0.3)                        
 htmltools          0.5.1.1    2021-01-22 [1] CRAN (R 4.0.3)                        
 httr               1.4.2      2020-07-20 [1] CRAN (R 4.0.2)                        
 igraph             1.2.6      2020-10-06 [1] CRAN (R 4.0.2)                        
 insight            0.14.2     2021-06-22 [1] CRAN (R 4.1.0)                        
 IRanges            2.26.0     2021-05-19 [1] Bioconductor                          
 iterators          1.0.13     2020-10-15 [1] CRAN (R 4.0.2)                        
 jsonlite           1.7.2      2020-12-09 [1] CRAN (R 4.0.2)                        
 kableExtra       * 1.3.4      2021-02-20 [1] CRAN (R 4.0.3)                        
 knitr              1.33       2021-04-24 [1] CRAN (R 4.0.3)                        
 labeling           0.4.2      2020-10-20 [1] CRAN (R 4.0.2)                        
 lattice            0.20-44    2021-05-02 [1] CRAN (R 4.0.3)                        
 lazyeval           0.2.2      2019-03-15 [1] CRAN (R 4.0.2)                        
 lifecycle          1.0.0      2021-02-15 [1] CRAN (R 4.0.3)                        
 lubridate          1.7.10     2021-02-26 [1] CRAN (R 4.0.3)                        
 magrittr           2.0.1      2020-11-17 [1] CRAN (R 4.0.2)                        
 MASS               7.3-54     2021-05-03 [1] CRAN (R 4.0.3)                        
 Matrix             1.3-4      2021-06-01 [1] CRAN (R 4.1.0)                        
 metacoder        * 0.3.5      2021-07-15 [1] Github (grunwaldlab/metacoder@8146849)
 mgcv               1.8-36     2021-06-01 [1] CRAN (R 4.1.0)                        
 modelr             0.1.8      2020-05-19 [1] CRAN (R 4.0.2)                        
 multcomp           1.4-17     2021-04-29 [1] CRAN (R 4.0.3)                        
 multtest           2.48.0     2021-05-19 [1] Bioconductor                          
 munsell            0.5.0      2018-06-12 [1] CRAN (R 4.0.2)                        
 mvtnorm            1.1-2      2021-06-07 [1] CRAN (R 4.1.0)                        
 nlme               3.1-152    2021-02-04 [1] CRAN (R 4.0.3)                        
 parameters         0.14.0     2021-05-29 [1] CRAN (R 4.1.0)                        
 patchwork        * 1.1.1      2020-12-17 [1] CRAN (R 4.0.2)                        
 permute            0.9-5      2019-03-12 [1] CRAN (R 4.0.2)                        
 phyloseq         * 1.27.6     2021-07-15 [1] Github (joey711/phyloseq@dc35470)     
 pillar             1.6.1      2021-05-16 [1] CRAN (R 4.0.3)                        
 pkgconfig          2.0.3      2019-09-22 [1] CRAN (R 4.0.2)                        
 plyr               1.8.6      2020-03-03 [1] CRAN (R 4.0.2)                        
 png                0.1-7      2013-12-03 [1] CRAN (R 4.0.2)                        
 purrr            * 0.3.4      2020-04-17 [1] CRAN (R 4.0.2)                        
 R6                 2.5.0      2020-10-28 [1] CRAN (R 4.0.2)                        
 Rcpp               1.0.7      2021-07-07 [1] CRAN (R 4.1.0)                        
 RCurl              1.98-1.3   2021-03-16 [1] CRAN (R 4.0.3)                        
 readr            * 2.0.0      2021-07-20 [1] CRAN (R 4.1.0)                        
 readxl             1.3.1      2019-03-13 [1] CRAN (R 4.0.2)                        
 reprex             2.0.0      2021-04-02 [1] CRAN (R 4.0.3)                        
 reshape2           1.4.4      2020-04-09 [1] CRAN (R 4.0.2)                        
 rhdf5              2.36.0     2021-05-19 [1] Bioconductor                          
 rhdf5filters       1.4.0      2021-05-19 [1] Bioconductor                          
 Rhdf5lib           1.14.2     2021-07-06 [1] Bioconductor                          
 rlang              0.4.11     2021-04-30 [1] CRAN (R 4.0.3)                        
 rmarkdown        * 2.9        2021-06-15 [1] CRAN (R 4.1.0)                        
 rprojroot          2.0.2      2020-11-15 [1] CRAN (R 4.0.2)                        
 rstudioapi         0.13       2020-11-12 [1] CRAN (R 4.0.2)                        
 Rttf2pt1           1.3.9      2021-07-22 [1] CRAN (R 4.1.0)                        
 rvest              1.0.0      2021-03-09 [1] CRAN (R 4.0.3)                        
 S4Vectors          0.30.0     2021-05-19 [1] Bioconductor                          
 sandwich           3.0-1      2021-05-18 [1] CRAN (R 4.0.3)                        
 scales           * 1.1.1      2020-05-11 [1] CRAN (R 4.0.2)                        
 see              * 0.6.4      2021-05-29 [1] CRAN (R 4.1.0)                        
 sessioninfo        1.1.1      2018-11-05 [1] CRAN (R 4.0.2)                        
 speedyseq        * 0.5.3.9001 2020-10-27 [1] Github (mikemc/speedyseq@8daed32)     
 stringi            1.7.3      2021-07-16 [1] CRAN (R 4.1.0)                        
 stringr          * 1.4.0      2019-02-10 [1] CRAN (R 4.0.2)                        
 survival           3.2-11     2021-04-26 [1] CRAN (R 4.0.3)                        
 svglite          * 2.0.0      2021-02-20 [1] CRAN (R 4.1.0)                        
 systemfonts        1.0.2      2021-05-11 [1] CRAN (R 4.0.3)                        
 TH.data            1.0-10     2019-01-21 [1] CRAN (R 4.0.2)                        
 tibble           * 3.1.2      2021-05-16 [1] CRAN (R 4.0.3)                        
 tidyr            * 1.1.3      2021-03-03 [1] CRAN (R 4.0.3)                        
 tidyselect         1.1.1      2021-04-30 [1] CRAN (R 4.0.3)                        
 tidyverse        * 1.3.1      2021-04-15 [1] CRAN (R 4.0.3)                        
 tzdb               0.1.2      2021-07-20 [1] CRAN (R 4.1.0)                        
 utf8               1.2.1      2021-03-12 [1] CRAN (R 4.0.3)                        
 vctrs              0.3.8      2021-04-29 [1] CRAN (R 4.0.3)                        
 vegan              2.5-7      2020-11-28 [1] CRAN (R 4.0.3)                        
 viridis          * 0.6.1      2021-05-11 [1] CRAN (R 4.0.3)                        
 viridisLite      * 0.4.0      2021-04-13 [1] CRAN (R 4.0.3)                        
 vroom              1.5.3      2021-07-14 [1] CRAN (R 4.1.0)                        
 webshot            0.5.2      2019-11-22 [1] CRAN (R 4.0.2)                        
 withr              2.4.2      2021-04-18 [1] CRAN (R 4.0.3)                        
 xfun               0.24       2021-06-15 [1] CRAN (R 4.1.0)                        
 xml2               1.3.2      2020-04-23 [1] CRAN (R 4.0.2)                        
 xtable             1.8-4      2019-04-21 [1] CRAN (R 4.0.2)                        
 XVector            0.32.0     2021-05-19 [1] Bioconductor                          
 yaml               2.2.1      2020-02-01 [1] CRAN (R 4.0.2)                        
 zlibbioc           1.38.0     2021-05-19 [1] Bioconductor                          
 zoo                1.8-9      2021-03-09 [1] CRAN (R 4.0.3)                        

[1] /home/angel/R/library
[2] /usr/local/lib/R/site-library
[3] /usr/lib/R/site-library
[4] /usr/lib/R/library

References

Foster, Zachary S. L., Thomas J. Sharpton, and Niklaus J. Grünwald. 2017. “Metacoder: An R Package for Visualization and Manipulation of Community Taxonomic Diversity Data.” PLOS Computational Biology 13 (2): e1005404. https://doi.org/10.1371/journal.pcbi.1005404.

Thompson, Luke R., Jon G. Sanders, Daniel McDonald, Amnon Amir, Joshua Ladau, Kenneth J. Locey, Robert J. Prill, et al. 2017. “A Communal Catalogue Reveals Earth’s Multiscale Microbial Diversity.” Nature 551 (7681): 457–63. https://doi.org/10.1038/nature24621.